Explaining the
diversity of
gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene
duplication and loss, but in prokaryotes, lateral gene transfer (LGT) can also contribute substantially to genome contents. To determine the histories of gene inventories, we conducted an exhaustive analysis of gene phylogenies for all gene
families in a widely sampled group, the -Proteobacteria. We show that, although these bacterial
genomes display striking differences in gene repertoires, most gene families having representatives in several species have congruent histories. Other than the few vast multigene families, gene duplication has contributed relatively little to the contents of these genomes; instead, LGT, over time, provides most of the diversity in
genomic repertoires. Most such acquired genes are lost, but the majority of those that persist in genomes are transmitted strictly vertically. Although our analyses are limited to the -Proteobacteria, these results resolve a long-standing paradoxi.e., the ability to make robust phylogenetic inferences in light of substantial LGT.
More abstracts about the Evolutionary Origins of Genomic Repertoires in Bacteria